VDJ demo subsample comparison

Author: Biqing Li

April 10, 2020

Background

To access how many reads are sufficient for confidently call VDJ chain type. I subsampled 0.17, 0.33, 0.50, 0.67, 0.83 and 1 of the total VDJ reads from the VDJ demo data. Then I compared the performance from the following aspects

Overall summary metrics Table



BCR_reads TCR_reads mRNA_reads BCR_reads_per_cell TCR_reads_per_cell mRNA_reads_per_cell No. Cell
0.17 1820500 3122026 7795724 677.0 1161.0 2899.1 2689
0.33 3536562 6065149 7795724 1352.9 2320.3 2982.3 2614
0.50 5360966 9192825 7795724 2050.9 3516.8 2982.3 2614
0.67 7183869 12324310 7795724 2721.2 4668.3 2952.9 2640
0.83 8899642 15268995 7795724 3437.5 5897.6 3011.1 2589
1 10722634 18398174 7795724 4077.0 6995.5 2964.2 2630

Overall summary metrics Figure

VDJ summary metrics Table



0.17 0.33 0.50 0.67 0.83 1
Reads_Cellular_Aligned_to_VDJ 3990815.00 7751682.00 11748252.00 15747435.00 19511039.00 23508003.00
Reads_CDR3_Valid_Unfiltered 3135000.00 6089575.00 9229733.00 12372514.00 15330701.00 18472896.00
Reads_CDR3_Valid_Putative 2799438.00 5279049.00 8035262.00 10882897.00 13208413.00 16154927.00
Pct_Reads_CDR3_Valid_from_Putative_Cells 89.30 86.69 87.06 87.96 86.16 87.45
Reads_CDR3_Valid_Putative_Corrected 2605679.00 4910067.00 7475808.00 10151168.00 12334222.00 15074284.00
Pct_Reads_CDR3_Valid_Corrected_from_Putative_Cells 83.12 80.63 81.00 82.05 80.45 81.60
Mean_Reads_CDR3_Valid_Corrected_per_Putative_Cell 969.01 1878.37 2859.91 3845.14 4764.09 5731.67
Molecules_Unfiltered 86790.00 120888.00 152504.00 182416.00 209337.00 237544.00
Molecules_Corrected_Putative 40017.00 43808.00 47067.00 50209.00 51506.00 53779.00
Mean_Molecules_Corrected_per_Putative_Cell 14.88 16.76 18.01 19.02 19.89 20.45

VDJ summary metrics Figure

Number of chain molecules Table





0.17 0.33 0.50 0.67 0.83 1
BCR_Heavy 9651 10656 11413 12305 12784 13250
BCR_Kappa 8703 9622 10212 10574 10867 11133
BCR_Lambda 5999 6487 6844 7044 7225 7381
TCR_Alpha 5877 6276 6893 7537 7656 8230
TCR_Beta 7989 8724 9464 10353 10472 11145
TCR_Delta 591 652 746 788 825 862
TCR_Gamma 1207 1391 1495 1608 1677 1778

Number of chain molecules Figure

Number of T&B cell with paired chains Table





0.17 0.33 0.50 0.67 0.83 1
T_CD4_memory 451 409 427 447 424 445
T_CD4_naive 273 264 269 283 270 280
T_CD8_memory 171 167 167 171 167 169
T_CD8_naive 95 92 92 96 94 96
T_gamma_delta 52 51 55 52 54 54
B 232 238 239 240 241 242

Number of T&B cell with paired chains Figure

Overlap of VDJ genotype - B cell

Overlap of VDJ genotype - Gamma Delta T cell

Overlap of VDJ genotype - CD4 memory T cell

Overlap of VDJ genotype - CD4 naive T cell

Overlap of VDJ genotype - CD8 memory T cell

Overlap of VDJ genotype - CD8 naive T cell

Gamma delta T cell - Gamma chain genotype

The cell with any void V/D/J segment will be removed

Gamma delta T cell - Gamma chain genotype 3Dbar

Gamma delta T cell - 3D movie

Gamma delta T cell - Gamma chain genotype Heatmap

Gamma delta T cell - Delta chain genotype

The cell with any void V/D/J segment will be removed

Gamma delta T cell - Delta chain genotype dotplot

Thank you!